null Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vk8-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:15 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 266 and 0 Target number of residues in the AU: 266 Target solvent content: 0.6199 Checking the provided sequence file Detected sequence length: 106 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 424 Adjusted target solvent content: 0.39 Input MTZ file: 1vk8-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.55 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 41.711 3.600 Wilson plot Bfac: 61.01 4070 reflections ( 95.85 % complete ) and 0 restraints for refining 3776 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.2956 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2786 (Rfree = 0.000) for 3776 atoms. Found 24 (24 requested) and removed 53 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.84 Search for helices and strands: 0 residues in 0 chains, 3836 seeds are put forward NCS extension: 0 residues added, 3836 seeds are put forward Round 1: 128 peptides, 27 chains. Longest chain 7 peptides. Score 0.268 Round 2: 185 peptides, 33 chains. Longest chain 15 peptides. Score 0.409 Round 3: 201 peptides, 34 chains. Longest chain 15 peptides. Score 0.456 Round 4: 207 peptides, 34 chains. Longest chain 12 peptides. Score 0.479 Round 5: 215 peptides, 34 chains. Longest chain 17 peptides. Score 0.509 Taking the results from Round 5 Chains 34, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7227 restraints for refining 3074 atoms. 6537 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2175 (Rfree = 0.000) for 3074 atoms. Found 13 (19 requested) and removed 48 (9 requested) atoms. Cycle 2: After refmac, R = 0.2078 (Rfree = 0.000) for 2993 atoms. Found 12 (19 requested) and removed 26 (9 requested) atoms. Cycle 3: After refmac, R = 0.1902 (Rfree = 0.000) for 2961 atoms. Found 11 (19 requested) and removed 34 (9 requested) atoms. Cycle 4: After refmac, R = 0.1849 (Rfree = 0.000) for 2931 atoms. Found 12 (18 requested) and removed 18 (9 requested) atoms. Cycle 5: After refmac, R = 0.1622 (Rfree = 0.000) for 2918 atoms. Found 9 (18 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.86 Search for helices and strands: 0 residues in 0 chains, 3052 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3072 seeds are put forward Round 1: 173 peptides, 35 chains. Longest chain 12 peptides. Score 0.322 Round 2: 184 peptides, 32 chains. Longest chain 11 peptides. Score 0.423 Round 3: 177 peptides, 30 chains. Longest chain 13 peptides. Score 0.429 Round 4: 178 peptides, 30 chains. Longest chain 11 peptides. Score 0.433 Round 5: 173 peptides, 27 chains. Longest chain 13 peptides. Score 0.465 Taking the results from Round 5 Chains 27, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7293 restraints for refining 3009 atoms. 6736 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1830 (Rfree = 0.000) for 3009 atoms. Found 13 (19 requested) and removed 33 (9 requested) atoms. Cycle 7: After refmac, R = 0.1687 (Rfree = 0.000) for 2972 atoms. Found 12 (19 requested) and removed 21 (9 requested) atoms. Cycle 8: After refmac, R = 0.1716 (Rfree = 0.000) for 2954 atoms. Found 10 (19 requested) and removed 21 (9 requested) atoms. Cycle 9: After refmac, R = 0.1637 (Rfree = 0.000) for 2937 atoms. Found 13 (18 requested) and removed 27 (9 requested) atoms. Cycle 10: After refmac, R = 0.1650 (Rfree = 0.000) for 2920 atoms. Found 15 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 3061 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3082 seeds are put forward Round 1: 137 peptides, 30 chains. Longest chain 9 peptides. Score 0.252 Round 2: 176 peptides, 31 chains. Longest chain 15 peptides. Score 0.407 Round 3: 191 peptides, 34 chains. Longest chain 12 peptides. Score 0.416 Round 4: 186 peptides, 33 chains. Longest chain 12 peptides. Score 0.413 Round 5: 168 peptides, 29 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 3 Chains 34, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6983 restraints for refining 2990 atoms. 6389 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1642 (Rfree = 0.000) for 2990 atoms. Found 11 (19 requested) and removed 22 (9 requested) atoms. Cycle 12: After refmac, R = 0.1506 (Rfree = 0.000) for 2969 atoms. Found 10 (19 requested) and removed 19 (9 requested) atoms. Cycle 13: After refmac, R = 0.1498 (Rfree = 0.000) for 2949 atoms. Found 15 (18 requested) and removed 17 (9 requested) atoms. Cycle 14: After refmac, R = 0.1553 (Rfree = 0.000) for 2943 atoms. Found 11 (18 requested) and removed 19 (9 requested) atoms. Cycle 15: After refmac, R = 0.1478 (Rfree = 0.000) for 2928 atoms. Found 12 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.78 Search for helices and strands: 0 residues in 0 chains, 3070 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3085 seeds are put forward Round 1: 143 peptides, 32 chains. Longest chain 6 peptides. Score 0.241 Round 2: 153 peptides, 30 chains. Longest chain 9 peptides. Score 0.326 Round 3: 163 peptides, 31 chains. Longest chain 10 peptides. Score 0.352 Round 4: 172 peptides, 32 chains. Longest chain 15 peptides. Score 0.373 Round 5: 163 peptides, 30 chains. Longest chain 11 peptides. Score 0.370 Taking the results from Round 4 Chains 32, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7379 restraints for refining 3068 atoms. 6851 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1745 (Rfree = 0.000) for 3068 atoms. Found 19 (19 requested) and removed 35 (9 requested) atoms. Cycle 17: After refmac, R = 0.1701 (Rfree = 0.000) for 3037 atoms. Found 18 (19 requested) and removed 19 (9 requested) atoms. Cycle 18: After refmac, R = 0.1779 (Rfree = 0.000) for 3026 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 19: After refmac, R = 0.1529 (Rfree = 0.000) for 3021 atoms. Found 16 (19 requested) and removed 19 (9 requested) atoms. Cycle 20: After refmac, R = 0.1660 (Rfree = 0.000) for 3011 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 3137 seeds are put forward NCS extension: 0 residues added, 3137 seeds are put forward Round 1: 160 peptides, 34 chains. Longest chain 9 peptides. Score 0.282 Round 2: 162 peptides, 29 chains. Longest chain 15 peptides. Score 0.384 Round 3: 169 peptides, 32 chains. Longest chain 10 peptides. Score 0.360 Round 4: 170 peptides, 30 chains. Longest chain 10 peptides. Score 0.400 Round 5: 163 peptides, 30 chains. Longest chain 10 peptides. Score 0.370 Taking the results from Round 4 Chains 30, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7050 restraints for refining 2988 atoms. 6520 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1746 (Rfree = 0.000) for 2988 atoms. Found 14 (19 requested) and removed 25 (9 requested) atoms. Cycle 22: After refmac, R = 0.1668 (Rfree = 0.000) for 2966 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 23: After refmac, R = 0.1521 (Rfree = 0.000) for 2961 atoms. Found 17 (19 requested) and removed 15 (9 requested) atoms. Cycle 24: After refmac, R = 0.1639 (Rfree = 0.000) for 2957 atoms. Found 17 (19 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1426 (Rfree = 0.000) for 2960 atoms. Found 13 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.85 Search for helices and strands: 0 residues in 0 chains, 3071 seeds are put forward NCS extension: 0 residues added, 3071 seeds are put forward Round 1: 121 peptides, 27 chains. Longest chain 7 peptides. Score 0.234 Round 2: 135 peptides, 27 chains. Longest chain 13 peptides. Score 0.301 Round 3: 143 peptides, 27 chains. Longest chain 9 peptides. Score 0.338 Round 4: 143 peptides, 27 chains. Longest chain 13 peptides. Score 0.338 Round 5: 161 peptides, 28 chains. Longest chain 14 peptides. Score 0.398 Taking the results from Round 5 Chains 28, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7308 restraints for refining 3051 atoms. 6804 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1625 (Rfree = 0.000) for 3051 atoms. Found 10 (19 requested) and removed 25 (9 requested) atoms. Cycle 27: After refmac, R = 0.1648 (Rfree = 0.000) for 3021 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 28: After refmac, R = 0.1532 (Rfree = 0.000) for 3013 atoms. Found 14 (19 requested) and removed 20 (9 requested) atoms. Cycle 29: After refmac, R = 0.1381 (Rfree = 0.000) for 2998 atoms. Found 12 (19 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1451 (Rfree = 0.000) for 2996 atoms. Found 18 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.98 Search for helices and strands: 0 residues in 0 chains, 3124 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3138 seeds are put forward Round 1: 126 peptides, 29 chains. Longest chain 7 peptides. Score 0.218 Round 2: 145 peptides, 29 chains. Longest chain 8 peptides. Score 0.309 Round 3: 150 peptides, 28 chains. Longest chain 11 peptides. Score 0.351 Round 4: 160 peptides, 29 chains. Longest chain 12 peptides. Score 0.376 Round 5: 156 peptides, 26 chains. Longest chain 11 peptides. Score 0.414 Taking the results from Round 5 Chains 26, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7312 restraints for refining 3075 atoms. 6818 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1556 (Rfree = 0.000) for 3075 atoms. Found 12 (19 requested) and removed 26 (9 requested) atoms. Cycle 32: After refmac, R = 0.1505 (Rfree = 0.000) for 3056 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 33: After refmac, R = 0.1484 (Rfree = 0.000) for 3043 atoms. Found 16 (19 requested) and removed 11 (9 requested) atoms. Cycle 34: After refmac, R = 0.1555 (Rfree = 0.000) for 3040 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 35: After refmac, R = 0.1057 (Rfree = 0.000) for 3042 atoms. Found 2 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 3147 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3159 seeds are put forward Round 1: 116 peptides, 26 chains. Longest chain 6 peptides. Score 0.229 Round 2: 130 peptides, 24 chains. Longest chain 10 peptides. Score 0.337 Round 3: 124 peptides, 22 chains. Longest chain 11 peptides. Score 0.350 Round 4: 121 peptides, 21 chains. Longest chain 9 peptides. Score 0.356 Round 5: 134 peptides, 22 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 5 Chains 22, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7215 restraints for refining 2994 atoms. 6789 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1528 (Rfree = 0.000) for 2994 atoms. Found 7 (19 requested) and removed 14 (9 requested) atoms. Cycle 37: After refmac, R = 0.1771 (Rfree = 0.000) for 2983 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 38: After refmac, R = 0.1666 (Rfree = 0.000) for 2973 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 39: After refmac, R = 0.1005 (Rfree = 0.000) for 2975 atoms. Found 3 (19 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.0862 (Rfree = 0.000) for 2961 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.90 Search for helices and strands: 0 residues in 0 chains, 3041 seeds are put forward NCS extension: 0 residues added, 3041 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 8 peptides. Score 0.272 Round 2: 114 peptides, 22 chains. Longest chain 9 peptides. Score 0.302 Round 3: 118 peptides, 22 chains. Longest chain 9 peptides. Score 0.322 Round 4: 119 peptides, 21 chains. Longest chain 9 peptides. Score 0.347 Round 5: 116 peptides, 19 chains. Longest chain 10 peptides. Score 0.373 Taking the results from Round 5 Chains 19, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7087 restraints for refining 2960 atoms. 6718 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1605 (Rfree = 0.000) for 2960 atoms. Found 15 (18 requested) and removed 17 (9 requested) atoms. Cycle 42: After refmac, R = 0.1443 (Rfree = 0.000) for 2954 atoms. Found 11 (18 requested) and removed 17 (9 requested) atoms. Cycle 43: After refmac, R = 0.1580 (Rfree = 0.000) for 2944 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 44: After refmac, R = 0.1458 (Rfree = 0.000) for 2946 atoms. Found 12 (18 requested) and removed 15 (9 requested) atoms. Cycle 45: After refmac, R = 0.1024 (Rfree = 0.000) for 2940 atoms. Found 2 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 3026 seeds are put forward NCS extension: 0 residues added, 3026 seeds are put forward Round 1: 121 peptides, 25 chains. Longest chain 8 peptides. Score 0.275 Round 2: 133 peptides, 25 chains. Longest chain 11 peptides. Score 0.332 Round 3: 116 peptides, 21 chains. Longest chain 9 peptides. Score 0.333 Round 4: 114 peptides, 22 chains. Longest chain 9 peptides. Score 0.302 Round 5: 116 peptides, 18 chains. Longest chain 14 peptides. Score 0.393 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vk8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4070 reflections ( 95.85 % complete ) and 7075 restraints for refining 2981 atoms. 6701 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1347 (Rfree = 0.000) for 2981 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1144 (Rfree = 0.000) for 2969 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1697 (Rfree = 0.000) for 2958 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1604 (Rfree = 0.000) for 2944 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:15:27 GMT 2018 Job finished. TimeTaking 52.37 Used memory is bytes: 3032384